Role of water molecules on the structure and

role of water molecules on the structure and stability of
hydrated GT. The microsolvation of GT with 11 water
molecules aids the formation of the folded structure.
Vibrational frequencies were computed to confirm
whether all the optimised structures are in stationary state.
The presence and strength of H-bonds were identified
and analysed through the interaction energies, and the
interaction energy was found to be larger for the
complexes with strong H-bonds. The calculated topologi-
cal parameters show the existence of strong H-bonds
associated with maximum electron density and higher
Table 6. NMR chemical shift values (in ppm) for the carbon atoms of bare and hydrated GT
n
. . . 4W n ¼ 1–5 and GT . . . 11W
complexes calculated at the B3LYP/6-311G (2d,2p) level of theory.
Sites
Complex C1 C3 C11 C14 C18 C21
GT1 51.06 172.22 41.58 165.36 38.73 170.12
GT1 . . . 4W 46.96 178.99 44.46 174.40 41.69 174.10
GT2 50.19 174.45 43.13 166.85 40.90 168.52
GT2 . . . 4W 46.54 177.62 44.39 173.27 39.81 170.85
GT3 50.08 174.29 43.17 168.65 42.28 168.46
GT3 . . . 4W 47.91 171.34 40.33 178.81 42.99 175.08
GT4 50.22 173.67 45.73 181.31 48.72 168.43
GT4 . . . 4W 46.18 179.49 42.89 172.30 39.88 170.59
GT5 49.60 184.39 47.04 187.55 69.08 180.70
GT5 . . . 4W 47.44 170.15 38.94 175.83 43.38 176.77
GT5 . . . 11W 42.01 165.90 41.16 175.67 45.61 178.61
Note: For labelling of atoms, refer Figure 5 .
Figure 13. Electrostatic potential map of GT5 and GT5 . . . (W)
n
n ¼ 4 and 11 complexes.
956 B. Yogeswari et al.
Downloaded by [Thammasat University Libraries] at 03:39 08 October 2014

stability. The NBO analysis yields larger value of
stabilisation energy (46.41 kcal/mol) for the interaction
between lone pairs of the acceptor atoms O(W) and BD
*
(O Z H(GT)) in the most stable GT5 . . . 4W complex. The
NMR calculations show that the C v O carbons of the first
and middle glycine fragments have maximum chemical
shifts in isolated GT and the chemical shift values of C
a
carbons were found to be the same due to the presence of
similar environment.
Acknowledgements
The authors R. Kanakaraju and B. Yogeswari gratefully thank
the University Grants Commission, New Delhi, India, for
the financial support in the form of Major Research Project
(No. 40-436/2011 (SR)).
References
[1] Ahn DS, Park SW, Jeon IS, Lee MK, Kim NH, Kim YH, Han YH,
Lee S. Effects of microsolvation on the structures and reactions of
neutral and zwitterionic alanine: computational study. J Phys Chem B.
2003;107:14109–14118.
[2] Halle B. Protein hydration dynamics in solution: a critical survey.
Philos Trans Soc Lond B. 2004;359:1207–1224.
[3] Creighton T. Proteins. 2nd ed. New York: Freeman and company;
1993.
[4] Baker EN. Solvent interactions with proteins as revealed by X-ray
crystallographic studies. In protein-solvent interactions. New York:
Marcel Dekker; 1995.
[5] Daniel RM, Dunn RV, Finney JL, Smith JC. The role of dynamics in
enzyme activity. Annu Rev Biophys Biomol Struct. 2003;32:69–92.
[6] Langhorst U, Backmann J, Loris R, Stevaert J. Analysis of water
mediated protein-protein interactions within RNase T1. Biochem-
istry. 2000;39:6586–6593.
[7] Denisov VP, Jonsson BH, Halle B. Hydration of denaturated and
molten globule proteins. Nat Struct Biol. 1999;6:253–260.